Modern wheat varieties grown with inorganic fertiliser show markedly fewer beneficial root bacteria compared to their unfertilised counterparts. In contrast, ancestral wheats show no such reduction, whether fertilised or not. This suggests modern cultivars have been bred to rely on nutritional inputs to maintain yields, a practice which reduces soil health.

The study highlights the potential of harnessing beneficial microbes and plant genetics to transition to lower-input farming systems.

Modern wheats have complex genomes with either four (tetraploid) or six (hexaploid) sets of chromosomes due to extensive crossing and interbreeding. Ancestral varieties, however, have simpler genomes with only two (diploid) sets of chromosomes.

The research team performed controlled experiments to compare growth-promoting root bacteria (plant growth-promoting rhizobacteria or PGPR) associated with diploid, tetraploid, and hexaploid wheats grown in both fertilised and unfertilised soil, resulting in the isolation of over 14,000 bacterial isolates.

“Modern wheat varieties have been bred to thrive in high-input systems”, said Dr Tessa Reid, the study’s lead researcher. “This appears to have greatly reduced the numbers of beneficial bacteria living on or around their root system. If we are to move to lower input systems, we will need to work out how to boost the abundance of beneficial soil microbes, so that they provide the nutritional benefits currently delivered by inorganic fertilisers.”

The team found that fertiliser application reduced the abundance of PGPR in polyploid wheats by 45%, making their levels no higher than in unplanted soil. This reduction was not observed in diploid wild wheats, the ancestors of modern varieties. Taxonomic analysis revealed this was largely driven by a reduced selection of beneficial root bacteria in modern wheats, especially from the phylum Bacteroidota.

“Microbiota of crop ancestors may offer a way to enhance sustainable food production,” said Dr Tim Mauchline, the team lead. “Future work could involve performing microbiome transplants, whereby, beneficial root microbes reduced through domestication, will be supplemented to modern wheat varieties. Alternatively, reintroducing key genetic traits to modern wheat, from their ancestors, to boost root colonisation of beneficial soil microbiota is another promising strategy.”